Table A1.

Comparison of presence calls.

Data Set	Replicate	TopHat (%)	MapAl (%)	In both (%)	TopHat only (%)	MapAl only (%)
1	1	54.5	67.4	51.1	3.3	16.2
	2	54.6	67.3	51.2	3.3	16.0
	3	54.2	67.1	50.9	3.2	16.1
2	1	51.8	62.1	46.6	5.3	15.5
	2	52.1	64.2	47.2	4.9	17.0
	3	52.2	64.6	47.4	4.7	17.1

For each data set and each replicate, the table shows the number of known splice forms identified by TopHat and MapAl. The majority of splice forms is seen by both pipelines. Additional reads spanning exon junctions, however, provide additional evidence for or against the presence of specific splice forms in MapAl, resulting in the differences observed.